Sensitive tissue-based detection of AR-V7 and other androgen receptor alterations using combined DNA/RNA comprehensive genomic profiling.
Authors: Zurita Amado J. , Gupta Shilpa , Graf Ryon P , Ross Jeffrey S. , Savol Andrej , Grinman Eddie , Allen Justin , Zhong Lei , Srivastava Abhishek , Wang Jue , Vagia Elena , Romann Josee D. , Cossis Kara , Huang Richard Sheng Poe , Keller-Evans Rachel B. 
Published: February 2025

195

Background:
Mechanisms of resistance to agents targeting the androgen receptor (AR) axis in prostate cancer (PC) include
AR
amplification (AMP), ligand-binding domain mutations (MUT), and splice variants (AR-Vs), such as AR-V7, which has been associated with resistance to the AR signaling inhibitors (ARSi) abiraterone and enzalutamide in castration resistant PC (CRPC). Clinically employed AR-V7 assays involve detection in circulating tumor cells (CTCs) based on either nuclear protein immunofluorescent staining or RNA expression. We sought to define the
AR
landscape of PC using DNA and RNA comprehensive genomic profiling (CGP) of tissue biopsies (TBx).
Methods:
We queried an institutional database (Foundation Medicine, Inc.) of CGP results. DNA and RNA co-extracted from formalin fixed paraffin embedded (FFPE) tumor TBx were profiled, respectively, using FoundationOne CDx (F1CDx) and FoundationOne RNA (F1RNA). AR-V7 positivity was defined by the presence of ≥10 unambiguous supporting reads in RNA. In DNA, AMP was defined as an amplification ratio of the modeled gene copy number to sample ploidy of ≥3.
Results:
94% (51/54) of PC FFPE samples underwent successful F1CDx + F1RNA, while 3 of 54 had inadequate RNA. The most commonly altered genes were
AR
(51.9%),
PTEN
(37.0%),
ERG
(25.9%),
TP53
(24.1%) and
SPOP
(13.0%).
AR
alterations were more prevalent in metastatic/non-primary tumor versus primary prostate biopsy sites (70.6% [12/17] vs 43.2% [16/37]). Notably, 6 AR-V7+ prostate tumors were confirmed as hormone naive. 82.1% (23/28) of
AR
-altered samples harbored AR-V7 with no other detected
AR
alteration, while 4 samples with AR-V7 harbored additional
AR
DNA alterations (3 w/ AMP, 1 w/ MUT), all of which were from secondary TBx sites.
Conclusions:
We describe the prevalence of
AR
alterations in PC TBx using F1CDx, which captures
AR
AMP and MUT in DNA, and F1RNA, which detects AR-V7 in RNA. The high prevalence of AR-V7 in secondary TBx sites in our cohort (>70%) reflects known increased expression associated with successive lines of anti-androgen/AR therapy. However, a high prevalence of AR-V7 was also detected in primary prostate biopsies (>40% compared to a reported <1% in CTCs), including in 6 hormone naive patients, suggesting sensitivity to detect low-level abundance even in hormone sensitive PC (HSPC). While detection of AR-V7 in CTCs suggests a patient may benefit from taxane chemotherapy over an ARSi in the setting of CRPC, the clinical significance in HSPC is not well understood. Clinical validation is required to determine the utility of AR-V7 detection in TBx using F1RNA in both the CRPC and HSPC settings. A combination DNA/RNA CGP strategy reporting on the spectrum of
AR
resistance alterations (AMP, MUT, AR-V7), along with non-
AR
genomic features, has the potential to enable informed use of ARSi and other agents at key decision nodes in PC patient care.