Early Dynamics of Quantitative SEPT9 and SHOX2 Methylation in Circulating Cell-Free Plasma DNA during Prostate Biopsy for Prostate Cancer Diagnosis

Abstract

Background: The methylation status of Septin 9 (SEPT9) and short stature homeobox 2 (SHOX2) in circulating cell-free DNA (ccfDNA) are validated pan-cancer biomarkers. The present proof-of-concept study aimed to investigate the potential and dynamics of quantitative SEPT9 and SHOX2 methylation in prostate cancer (PCa) patient tissue and ccfDNA during prostate biopsy as a diagnostic tool. Methods: The methylation patterns of SEPT9 and SHOX2 in prostate tissue were analyzed using The Cancer Genome Atlas data set (n = 498 PCa and n = 50 normal adjacent prostate tissue (NAT)). Next, dynamic changes of ccfDNA methylation were quantified in prospectively enrolled patients undergoing prostate biopsy (n = 72), local treatment for PCa (n = 7; radical prostatectomy and radiotherapy) as well as systemic treatment for PCa (n = 6; chemotherapy and 177-Lu-PSMA-therapy). Biomarker levels were correlated with clinicopathological parameters. Results: SEPT9 and SHOX2 were hypermethylated in PCa tissue (p < 0.001) and allowed discrimination of PCa and non-tumor prostate tissue (mSEPT9: AUC 0.87, 95%CI [0.82–0.92]; mSHOX2: AUC 0.89, 95%CI 0.84–0.94). SHOX2 methylation and mRNA levels were significantly higher in PCa tissue and increased with tumor stage and grade, as well as in patients suffering from biochemical recurrence following radical prostatectomy. SEPT9 and SHOX2 ccfDNA methylation allowed distinguishing patients with localized and metastatic disease (p < 0.001 for both). In addition, methylation levels increased shortly after prostate biopsy only in patients with PCa (ΔmSEPT9: p < 0.001 and ΔmSHOX2: p = 0.001). Conclusions: The early dynamics of methylated SEPT9 and SHOX2 in ccfDNA allow differentiation between PCa patients and patients without PCa and is a promising marker for tumor monitoring in the metastatic stage to determine tumor burden under systemic therapy.

Integrated analysis of single-cell and bulk RNA-sequencing reveals a novel signature based on NK cell marker genes to predict prognosis and immunotherapy response in gastric cancer

“…CYP19A1 , a member of the cytochrome P450 family, was previously found to be highly expressed in GC and associated with an adverse prognosis; the silencing of its expression could be useful for GC treatment 31 , 32 . A previous study showed that SHOX2 methylation represent a potential biomarker for some cancers 33 – 37 . This gene was also shown to be related to unfavorable distant metastasis-free survival and could promote WASF3 transcriptional activity to induce the growth and metastasis of breast cancer.…”

Evaluation of DNA methylation levels of SEPT9 and SHOX2 in plasma of patients with head and neck squamous cell carcinoma using droplet digital PCR

“…In this context, in a previous study, the post-therapeutic plasmatic circulating SHOX2 and SEPT9 methylation ccfDNA levels were decreased in patients with colorectal cancer with localized disease, while there was no decrease in patients with distant metastases ( 41 ). Furthermore, high methylation levels of circulating SEPT9 and SHOX2 characterized patients with metastatic disease in prostate cancer ( 47 ). In HNSCC, the baseline positivity of SEPT9 and SHOX2 methylation in plasma was identified in 15 patients (15/20, 75%), and methylation levels decreased with systemic therapy ( 40 ).…”

SHOX2 promotes prostate cancer proliferation and metastasis through disruption of the Hippo-YAP pathway

“… 31 In PCa, early changes in methylated SEPT9 and SHOX2 in circulating cell-free plasma DNA can differentiate between patients with and without PCa and serve as a promising marker for tumor monitoring during systemic therapy to determine tumor burden in the metastatic stage. 13 However, the mechanism by which SHOX2 regulates PCa progression remains unknown. In the present study, we found that SHOX2 levels were markedly elevated in PCa tissues compared to normal tissues.…”

“…Furthermore, recent studies have shown that the methylation level of SHOX2 enables differentiation between localized and metastatic disease in PCa patients, with a rise in levels shortly after biopsy. 13 However, despite these advances, the precise role played by SHOX2 in PCa biological processes is yet to be comprehensively understood.…”