Cell-Free DNA Analysis Could Aid in Detection, Optimal Management of Resistant Metastatic Prostate Cancer

Cell-free DNA (cfDNA)–based androgen receptor (AR) locus alterations and enhancers correlated with metastatic prostate cancers determined to be resistant to AR-targeted therapies, according to results of an analysis published in the JCO Precision Oncology.

The use of the plasma-based assay Enhancer and Neighboring Loci of Androgen Receptor Sequencing (EnhanceAR-Seq) to analyze cfDNA can reasonably be used to more accurately identify risk and disease resistance earlier on and create more personalized therapies for patients with metastatic prostate cancer.

“We think, right now, we're showing a very strong prognostic association and we're showing the ability to identify resistance,” explained co-author Aadel Chaudhuri, MD, PhD, an assistant professor of radiation oncology, Cancer Biology Division, and genetic at Washington University School of Medicine in St. Louis, in an interview with OncLive. “The next [focus] will be to identify these patients early and then [give them the best treatment]. Specifically, if we think these patients are resistant to AR-directed drugs, we can give them an alternate therapy [such as] chemotherapy, systemic radiotherapy, or immunotherapy to hopefully improve their outcomes.”

cfDNA and circulating tumor cell (CTC)-based liquid biopsies have risen as diagnostic tools in helping to guide AR-directed therapies in patients with metastatic prostate cancer. Challenges have comprised complex mechanisms and a need to better understand the genomic events that contribute toward metastatic prostate cancer. With underutilized current assays showing low sensitivity capabilities, the study investigators theorized that by utilizing cfDNA to track AR/enhancer genomic alterations, treatment-resistant disease can be detected with a higher sensitivity.

EnhanceAR-Seq helped investigators to identify genomic alterations in 45% of cases studied with a 40% rate of AR enhancer amplification. Additionally, it was noted that patients who had AR/enhancer alteration also had a notably worse outcome in terms of PFS and OS than those who lacked alterations, with 6-month progression-free survival (PFS) rates of 30% versus 71% (P = .0002), and 6-month overall survival (OS) rates of 59% at 100% (P = .0015). AR/enhancer alterations in plasma cfDNA additionally outperformed the CTC AR-V7 assay and was able to detect 78% (n = 18) of resistant disease cases.

“There are some patients who are outright resistant to [androgen receptor-targeted therapies],” said Chaudhuri. “Those patients, unfortunately, do very poorly. Their median survival, as we saw in the literature for these patients who are primarily resistant to AR-targeted drugs, was less than 6 months. We specifically asked, 'Can we identify these patients early, predict their resistance, predict their survival?' [If so], in the future, we can develop a trial act at that time point and do something about it.”

With 20% to 40% of patients developing primary resistance to AR-directed therapies and the current AR-V7 assay providing an approximate 30% sensitivity rate for detection, investigators suggested that cfDNA could prove to be a noninvasive and more sensitive method in prostate cancer. A set of wide-scale whole-genomic sequencing studies uncovered a long-range noncoding enhancer upsteam of AR that helps to not only promote expression, but also present resistance to AR-targeting treatments, with AR enhancer noted as amplifying in 81% to 87%; a genomic alteration in mCRPC was found to be the most frequently occurring.

Forty patients diagnosed with metastatic prostate cancer and had at least 1 month of prior standard AR-directed treatment were enrolled. Patients could have received prior systemic therapy but could not have active non-prostate malignancies. Plasma samples were provided for cfDNA analysis upon enrollment and continued to undergo clinical and laboratory follow-up over the course of the study.

EnhanceAR-Seq was developed as a targeted sequencing plasma cfDNA assay that can better identify alterations in the AR gene, enhancer loci, and other altered genes better than prior liquid biopsies. Primary resistance was defined by prostate-specific antigen (PSA) progression, change in treatment, death within 4 months of initiation, or radiographic progression after 6 months.

Aside from the 18 patients (45%) who tested positive for AR/enhancer alterations, an additional 3 (8%) were observed as having AR-enhancer amplification independent of AR gene body amplification. Six patients (15%) were also believed to have experienced copy number loss due to other cfDNA genes, such as TP53 and PTEN, which were targeted by alterations.

Ten metastatic tissue biopsies were analyzed through the same type of sequencing; results found that 5 samples exhibited evidence of AR gene body alteration with tumors and 4 within plasma. Therefore, results showed that the alterations were 80% concordant between tissue and plasma samples. These alterations within the AR locus were able to help investigators to predict resistant disease with 78% sensitivity and 100% specificity rates. Among the 3 patients who experienced AR enhancer amplification in cfDNA without amplification, all experienced progression to resistance at a median 5.3 months (range, 0.6-8.0 months).

PFS was additionally observed as being smaller in the 18 patients with AR/enhancer alterations than those who didn't (n = 22; HR, 6.8; 95% CI, 2.5-18.6; P = .0002). A decreased PFS and similar HR extended to AR enhancer region after investigators restricted the study (HR, 8.1; 95% CI, 2.8-23.6; P = .0001). Despite a shorter median follow-up time of 6 months, preliminary data showed that OS was found to be shorter in patients who had ER/enhancer alterations in their plasma cfDNA (HR, 11.5; 95% CI, 2.5-52.1; P = .0015)

"This is one more assay that's showing the power of using cfDNA liquid biopsies to identify oncogenomic alterations in the blood that associate strongly with outcomes,” said Chaudhuri. “Associations that we can act upon at an early time point in order to improve patients’ outcomes in a personalized and precise fashion. This is one more step towards our goal of improving cancer outcomes through personalized, precision medicine."

Reference

Dang HX, Chauhan PS, Ellis Haley, et al. Cell-free DNA alterations in the AR enhancer and locus predict resistance to AR-directed therapy in patients with metastatic prostate cancer [published online ahead of print June 18, 2020]. JCO Precis Oncol. 2020;4:680-713. doi:10.1200/PO.20.00047