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Background <p>We evaluated whether 5hmC signatures in cell-free DNA (cfDNA) are associated with treatment failure to androgen-deprivation therapies (ADT) among men with hormone-naive prostate cancer.</p> Methods <p>We collected a total of 139 serial plasma samples from 55 prostate cancer patients receiving ADT at 3 time points including baseline (before initiating ADT, <i>n</i> = 55); 3 months (after initiating ADT, <i>n</i> = 55); and disease progression (<i>n</i> = 15) within 24 months or 24 months if no progression was detected (<i>n</i> = 14). We used selective chemical labeling sequencing to quantify 5hmC abundance across the genome and Kaplan–Meier analysis to assess survival association.</p> Results <p>Here we show a significant 5hmC difference in 1642 of 23433 genes between patients with and without progression (false discovery rate [FDR] &lt; 0.1) in baseline plasma samples. Patients with progression demonstrate significant 5hmC enrichments in multiple hallmark gene sets, with androgen responses as the top enriched gene-set (FDR = 1.19E−13). We further show a significant association between high activity scores in these gene sets and poor progression-free survival (<i>P</i> &lt; 0.05), even after adjusting for circulating tumor DNA fraction and prostate-specific antigen values. Additionally, our longitudinal analysis shows that the high activity score is significantly reduced after 3 months of initiating ADT (<i>P</i> = 0.0004) but returns to higher levels when the disease progresses (<i>P</i> = 0.0317).</p> Conclusions <p>5hmC-based activity scores from gene-sets involved in <i>AR</i> responses show great potential in assessing treatment resistance, monitoring disease progression, and identifying patients who would benefit from upfront treatment intensification. However, further studies are needed to validate these findings.</p>

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5-hydroxymethylcytosine sequencing of plasma cell-free DNA identifies epigenomic features in prostate cancer patients receiving androgen deprivation therapies

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年3月4日

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  • Qianxia Li,
  • Chiang-Ching Huang,
  • Shane Huang,
  • Yijun Tian,
  • Jinyong Huang,
  • Amirreza Bitaraf,
  • Xiaowei Dong,
  • Marja T. Nevalainen,
  • Manishkumar Patel,
  • Jodie Wong,
  • Jingsong Zhang,
  • Brandon J. Manley,
  • Jong Y. Park,
  • Manish Kohli,
  • Elizabeth M. Gore,
  • Deepak Kilari,
  • Liang Wang

摘要

Background

We evaluated whether 5hmC signatures in cell-free DNA (cfDNA) are associated with treatment failure to androgen-deprivation therapies (ADT) among men with hormone-naive prostate cancer.

Methods

We collected a total of 139 serial plasma samples from 55 prostate cancer patients receiving ADT at 3 time points including baseline (before initiating ADT, n = 55); 3 months (after initiating ADT, n = 55); and disease progression (n = 15) within 24 months or 24 months if no progression was detected (n = 14). We used selective chemical labeling sequencing to quantify 5hmC abundance across the genome and Kaplan–Meier analysis to assess survival association.

Results

Here we show a significant 5hmC difference in 1642 of 23433 genes between patients with and without progression (false discovery rate [FDR] < 0.1) in baseline plasma samples. Patients with progression demonstrate significant 5hmC enrichments in multiple hallmark gene sets, with androgen responses as the top enriched gene-set (FDR = 1.19E−13). We further show a significant association between high activity scores in these gene sets and poor progression-free survival (P < 0.05), even after adjusting for circulating tumor DNA fraction and prostate-specific antigen values. Additionally, our longitudinal analysis shows that the high activity score is significantly reduced after 3 months of initiating ADT (P = 0.0004) but returns to higher levels when the disease progresses (P = 0.0317).

Conclusions

5hmC-based activity scores from gene-sets involved in AR responses show great potential in assessing treatment resistance, monitoring disease progression, and identifying patients who would benefit from upfront treatment intensification. However, further studies are needed to validate these findings.