Cell-free DNA alterations in the <i>AR</i> enhancer and locus predict resistance to AR-directed therapy in patients with metastatic prostate cancer.

Abstract

Cell-free DNA (cfDNA) and circulating tumor cell (CTC) based liquid biopsies have emerged as potential tools to predict responses to androgen receptor (AR)-directed therapy in metastatic prostate cancer. However, due to complex mechanisms and incomplete understanding of genomic events involved in metastatic prostate cancer resistance, current assays (e.g. CTC AR-V7) demonstrate low sensitivity and remain underutilized. The recent discovery of <i>AR</i> enhancer amplification in >80% of metastatic patients and its association with disease resistance presents an opportunity to improve upon current assays. We hypothesized that tracking <i>AR</i>/enhancer genomic alterations in plasma cfDNA would detect resistance with high sensitivity and specificity. We developed a targeted sequencing and analysis method as part of a new assay called Enhancer and neighboring loci of Androgen Receptor Sequencing (EnhanceAR-Seq). We applied EnhanceAR-Seq to plasma collected from 40 patients with metastatic prostate cancer treated with AR-directed therapy to monitor <i>AR</i>/enhancer genomic alterations and correlate these events with therapy resistance, progression-free survival (PFS) and overall survival (OS). EnhanceAR-Seq identified genomic alterations in the <i>AR</i>/enhancer locus in 45% of cases, including a 40% rate of <i>AR</i> enhancer amplification. Patients with <i>AR</i>/enhancer alterations had significantly worse PFS and OS than those without (6-month PFS: 30% vs. 71%, <i>P=0.0002</i>; 6-month OS: 59% vs. 100%, <i>P=0.0015</i>). <i>AR</i>/enhancer alterations in plasma cfDNA detected 18 of 23 resistant cases (78%) and outperformed the CTC AR-V7 assay which was also run on a subset of patients. cfDNA-based <i>AR</i> locus alterations, including of the enhancer, are strongly associated with resistance to AR-directed therapy and significantly worse survival. cfDNA analysis using EnhanceAR-Seq may enable more precise risk stratification and personalized therapeutic approaches for metastatic prostate cancer.