Assessment of radiotherapy effect and toxicity using tissue-associated DNA methylation markers in cell-free DNA: a study on prostate cancer.

Abstract

This study aimed to evaluate tissue-associated circulating cell-free DNA (cfDNA) as indicators of radiotherapy-related effects and treatment-associated toxicity in prostate cancer. In addition, inter-individual variability in these markers and their responses to radiotherapy-induced cystitis and rectitis were investigated. The DNA methylation status of six tissue-associated genes representing the prostate (KLK3, TGM4), colon (MUC2, MS4A12), and bladder (UPK2, DHRS2) was analyzed in serum-derived cfDNA using methylation-sensitive melting curve analysis (MS-MCA). Five of the six analyzed genes demonstrated significantly higher relative DNA levels in patients with prostate cancer compared with controls. Radiotherapy did not significantly alter the relative DNA levels of these tissue-associated genes. However, cfDNA fragmentation was significantly increased in the post-treatment group compared to the pre-treatment group. Notably, 79-bp DNA fragments were significantly more abundant than 230-bp fragments. In the post-treatment group, no significant correlations were observed between cfDNA fragmentation and the relative DNA levels of most targets, except for an association between the 230-bp fragment and TGM4 relative DNA levels. These findings suggest limited coupling between cfDNA fragmentation patterns and tissue-associated cfDNA release. Marked inter-individual variability in cfDNA methylation signatures was observed across all examined CpG-containing regions except UPK2. This variability did not change significantly following radiotherapy and may therefore limit the utility of these assay regions for monitoring individual radiation-induced tissue damage. Furthermore, no significant changes in methylation profiles of colon- or bladder-associated genes were detected in patients who developed radiotherapy-induced rectitis or cystitis. Overall, increased cfDNA fragmentation following radiotherapy and substantial inter-individual variability in methylation profiles across tissue-associated regions may mask tissue-associated cfDNA signals, thereby complicating the assessment of radiation-induced tissue damage.