Cell-Free DNA Variant Sequencing Using Plasma and AR-V7 Testing of Circulating Tumor Cells in Prostate Cancer Patients

Abstract

Prostate cancer (PCa) is the second most common malignant cancer and is a major cause of morbidity and mortality among men worldwide. There is still an urgent need for biomarkers applicable for diagnosis, prognosis, therapy prediction, or therapy monitoring in PCa. Liquid biopsies, including cell-free DNA (cfDNA) and circulating tumor cells (CTCs), are a valuable source for studying such biomarkers and are minimally invasive. In our study, we investigated the cfDNA of 34 progressive PCa patients, via targeted sequencing, for sequence variants and for the occurrence of CTCs, with a focus on androgen receptor splice variant 7 (AR-V7)-positive CTCs. The cfDNA content was associated with overall survival (OS; p = 0.014), disease-specific survival (DSS; p = 0.004), and time to treatment change (TTC; p = 0.001). Moreover, when considering all sequence variants grouped by their functional impact and allele frequency, a significant association with TTC (p = 0.017) was observed. When investigating only pathogenic or likely pathogenic gene variants, variants of the BRCA1 gene (p = 0.029) and the AR ligand-binding domain (p = 0.050) were associated with a shorter TTC. Likewise, the presence of CTCs was associated with a shorter TTC (p = 0.031). The presence of AR-V7-positive CTCs was associated with TTC (p < 0.001) in Kaplan–Meier analysis. Interestingly, all patients with AR-V7-positive CTCs also carried TP53 point mutations. Altogether, analysis of cfDNA and CTCs can provide complementary information that may support temporal and targeted treatment decisions and may elucidate the optimal choice within the variety of therapy options for advanced PCa patients.

Cell-Free DNA Sequencing Reveals Gene Variants in DNA Damage Repair Genes Associated with Prognosis of Prostate Cancer Patients

“…After stratifying the patients at the median of affected DDR genes with CPS variants (>4 vs. ≤4), those with >4 affected DDR genes with CPS variants showed a shorter TTC compared to patients with fewer DDR genes with CPS variants. This finding agreed with our previous result that patients with a higher number of gene variants have a shorter TTC in general [ 34 ]. We evaluated the association of gene variants in each DDR gene with OS or DSS, and we found that patients with gene variants in some DDR genes showed a better OS or DSS than patients without such gene variants.…”

“…The cfDNA of 34 PCa patients (39 samples) was evaluated for gene variants in 99 genes by NGS as described previously [ 34 ] and here in Table S2 . We investigated in a continued analysis, gene variants in DNA damage repair genes and their association with prognosis, i.e., OS, DSS or TTC.…”

“…The dataset underlying this analysis has been described in detail [ 34 ]. Briefly, targeted NGS sequencing was conducted using 39 samples of cfDNA originating from 34 PCa patients.…”